diff stacks_refmap.xml @ 12:d7a482f44e08 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb

--- a/stacks_refmap.xml	Tue Mar 22 23:18:13 2022 +0000
+++ b/stacks_refmap.xml	Fri Apr 07 22:02:19 2023 +0000
@@ -1,9 +1,9 @@
 <tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0">
     <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
@@ -151,8 +151,8 @@
             </when>
         </conditional>
 
-        <param name="m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" argument="-m" />
-        <param name="P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" argument="-P" />
+        <param argument="-m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" />
+        <param argument="-P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" />
 
         <!-- SNP Model options -->
         <section name="snp_options" title="SNP_Model_Options" expanded="False">